sp. nov., and gen. nov., sp. nov., carbon monoxide-oxidizing bacteria isolated from geothermally heated biofilms Free

Abstract

Two thermophilic, Gram-stain-positive, rod-shaped, non-spore-forming bacteria (strains KI3 and KI4) were isolated from geothermally heated biofilms growing on a tumulus in the Kilauea Iki pit crater on the flank of Kilauea Volcano (Hawai‘i, USA). Strain KI3 grew over an examined temperature range of 50–70 °C (no growth at 80 °C) and a pH range of 6.0–9.0, with optimum growth at 70 °C and pH 7.0. Strain KI4 grew at temperatures of 55–70 °C and a pH range of 5.8–8.0, with optimum growth at 65 °C and pH 6.7–7.1. The DNA G+C contents of strains KI3 and KI4 were 66.0 and 60.7 mol%, respectively. The major fatty acid for both strains was 12-methyl C. Polar lipids in strain KI3 were dominated by glycolipids and phosphatidylinositol, while phosphatidylinositol and phosphoglycolipids dominated in strain KI4. Strain KI3 oxidized carbon monoxide [6.7±0.8 nmol CO h (mg protein)], but strain KI4 did not. 16S rRNA gene sequence analyses determined that the strains belong to the class , and that strains KI3 and KI4 are related most closely to DSM 5159 (96.5 and 91.1 % similarity, respectively). 16S rRNA gene sequence similarity between strain KI3 and strain KI4 was 91.4 %. Phenotypic features and phylogenetic analyses supported the affiliation of strain KI3 to the genus , while results of chemotaxonomic, physiological and biochemical assays differentiated strains KI3 and KI4 from . Strain KI3 ( = DSM 27067 = ATCC BAA-2535) is thus considered to be the type strain of a novel species, for which the name sp. nov. is proposed. Additionally, the characterization and phylogenetic position of strain KI4 showed that it represents a novel species of a new genus, for which the name gen. nov., sp. nov. is proposed. The type strain of is KI4 ( = DSM 27169 = ATCC BAA-2536).

Funding
This study was supported by the:
  • National Science Foundation (Award NSF-MCB-0348100)
  • NASA
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.060327-0
2014-08-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/8/2586.html?itemId=/content/journal/ijsem/10.1099/ijs.0.060327-0&mimeType=html&fmt=ahah

References

  1. Bikandi J., San Millán R., Rementeria A., Garaizar J. ( 2004 ). In silico analysis of complete bacterial genomes: PCR, AFLP-PCR and endonuclease restriction. . Bioinformatics 20, 798799. [View Article] [PubMed]
    [Google Scholar]
  2. Botero L. M., Brown K. B., Brumefield S., Burr M., Castenholz R. W., Young M., McDermott T. R. ( 2004 ). Thermobaculum terrenum gen. nov., sp. nov.: a non-phototrophic gram-positive thermophile representing an environmental clone group related to the Chloroflexi (green non-sulfur bacteria) and Thermomicrobia . . Arch Microbiol 181, 269277. [View Article] [PubMed]
    [Google Scholar]
  3. Cashion P., Holder-Franklin M. A., McCully J., Franklin M. ( 1977 ). A rapid method for the base ratio determination of bacterial DNA. . Anal Biochem 81, 461466. [View Article] [PubMed]
    [Google Scholar]
  4. Duque C., Cepeda N., Martínez A. ( 1993 ). The steryl ester and phospholipid fatty acids of the sponge Agelas conifera from the Colombian Caribbean. . Lipids 28, 767769. [View Article]
    [Google Scholar]
  5. Edgar R. C. ( 2004 ). muscle: multiple sequence alignment with high accuracy and high throughput. . Nucleic Acids Res 32, 17921797. [View Article] [PubMed]
    [Google Scholar]
  6. Gupta R. S., Chander P., George S. ( 2013 ). Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades; proposal for division of the class Chloroflexia class. nov. into the suborder Chloroflexineae subord. nov., consisting of the emended family Oscillochloridaceae and the family Chloroflexaceae fam. nov., and the suborder Roseiflexineae subord. nov., containing the family Roseiflexaceae fam. nov.. Antonie van Leeuwenhoek 103, 99119. [View Article] [PubMed]
    [Google Scholar]
  7. Hugenholtz P., Stackebrandt E. ( 2004 ). Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). . Int J Syst Evol Microbiol 54, 20492051. [View Article] [PubMed]
    [Google Scholar]
  8. Jackson T. J., Ramaley R. F., Meinschein W. G. ( 1973 ). Thermomicrobium, a new genus of extremely thermophilic bacteria. . Int J Syst Bacteriol 23, 2836. [View Article]
    [Google Scholar]
  9. Kibbe W. A. ( 2007 ). OligoCalc: an online oligonucleotide properties calculator. . Nucleic Acids Res 35 (suppl 2), W43–46. [View Article] [PubMed]
    [Google Scholar]
  10. King G. M. ( 1999 ). Characteristics and significance of atmospheric carbon monoxide consumption by soils. . Chemosphere Glob Chang Sci 1, 5363. [View Article]
    [Google Scholar]
  11. King G. M., Weber C. F. ( 2008 ). Interactions between bacterial carbon monoxide and hydrogen consumption and plant development on recent volcanic deposits. . ISME J 2, 195203. [View Article] [PubMed]
    [Google Scholar]
  12. Kiss H., Cleland D., Lapidus A., Lucas S., Del Rio T. G., Nolan M., Tice H., Han C., Goodwin L. & other authors ( 2010 ). Complete genome sequence of ‘Thermobaculum terrenum’ type strain (YNP1). . Stand Genomic Sci 3, 153162. [View Article] [PubMed]
    [Google Scholar]
  13. Kunisawa T. ( 2011 ). The phylogenetic placement of the non-phototrophic, Gram-positive thermophile ‘Thermobaculum terrenum’ and branching orders within the phylum ‘Chloroflexi’ inferred from gene order comparisons. . Int J Syst Evol Microbiol 61, 19441953. [View Article] [PubMed]
    [Google Scholar]
  14. Kuykendall L. D., Roy M. A., O’Neill J. J., Devine T. E. ( 1988 ). Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum . . Int J Syst Bacteriol 38, 358361. [View Article]
    [Google Scholar]
  15. Lane D. J. ( 1991 ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115175. Edited by Stackebrandt E., Goodfellow M. . New York:: Wiley;.
    [Google Scholar]
  16. Mesbah M., Premachandran U., Whitman W. ( 1989 ). Precise measurement of the G+C content of deoxyribonucleic acid by high performance liquid chromatography. . Int J Syst Bacteriol 39, 159167. [View Article]
    [Google Scholar]
  17. Miller L. T. ( 1982 ). Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. . J Clin Microbiol 16, 584586.[PubMed]
    [Google Scholar]
  18. Pati A., Labutti K., Pukall R., Nolan M., Glavina Del Rio T., Tice H., Cheng J. F., Lucas S., Chen F. & other authors ( 2011 ). Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21). . Stand Genomic Sci 5, 97111. [View Article] [PubMed]
    [Google Scholar]
  19. Pruesse E., Peplies J., Glöckner F. O. ( 2012 ). sina: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. . Bioinformatics 28, 18231829. [View Article] [PubMed]
    [Google Scholar]
  20. Reasoner D. J., Geldreich E. E. ( 1985 ). A new medium for the enumeration and subculture of bacteria from potable water. . Appl Environ Microbiol 49, 17.[PubMed]
    [Google Scholar]
  21. Sambrook J., Russell D. W. ( 2001 ). Molecular Cloning: A Laboratory Manual, , 3rd edn.. New York:: Cold Spring Harbour Laboratory Press;.
    [Google Scholar]
  22. Scholfield C. R., Dutton H. J. ( 1971 ). Equivalent chain lengths of methyl octadecadienoates and octadecatrienoates. . J Am Oil Chem Soc 48, 228231. [View Article]
    [Google Scholar]
  23. Smibert R. M., Krieg N. L. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology Press;.
    [Google Scholar]
  24. Sorokin D. Y., Lücker S., Vejmelkova D., Kostrikina N. A., Kleerebezem R., Rijpstra W. I. C., Damsté J. S., Le Paslier D., Muyzer G. & other authors ( 2012 ). Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi . . ISME J 6, 22452256. [View Article] [PubMed]
    [Google Scholar]
  25. Takagi T., Itabashi Y. ( 1981 ). Occurrence of mixtures of geometrical isomers of conjugated octadecatrienoic acids in some seed oils: analysis by open-tubular gas liquid chromatography and high performance liquid chromatography. . Lipids 16, 546551. [View Article]
    [Google Scholar]
  26. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011 ). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28, 27312739. [View Article] [PubMed]
    [Google Scholar]
  27. Tindall B. J., Sikorski J., Smibert R. M., Kreig N. R. ( 2007 ). Phenotypic characterization and the principles of comparative systematics. . In Methods for General and Molecular Microbiology, , 3rd edn., pp. 330393. Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G., Schmidt T. M., Snyder L. R. . Washington, DC:: American Society for Microbiology;. [View Article]
    [Google Scholar]
  28. Wu D., Raymond J., Wu M., Chatterji S., Ren Q., Graham J. E., Bryant D. A., Robb F., Colman A. & other authors ( 2009 ). Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum . . PLoS ONE 4, e4207. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.060327-0
Loading
/content/journal/ijsem/10.1099/ijs.0.060327-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed